The impact of chemical to organic fertilizer substitution on soil labile organic and stabilized N pools under intensive farming systems is unclear. Therefore, we analyzed the distribution of soil total N (STN), particulate organic N (PON), microbial biomass N (MBN), dissolved organic N (DON), and mineral N (NO3− and NH4+) levels down to 100 cm profile under wheat–maize rotation system in northern China. The experiment was established with four 270 kg ha−1 N equivalent fertilizer treatments: Organic manure (OM); Organic manure with nitrogen fertilizer (OM + NF); Nitrogen fertilizer (NF); and Control (CK). Results found that the OM and OM + NF treatments had significantly higher STN, PON, MBN, DON, and NO3− contents in 0–20 cm topsoil depths. Conversely, the NF treatment resulted in the highest (p < 0.01) DON and NO3− depositions in 40–100 cm subsoil depths. The NH4+ contents in selected profile depths were significantly highest (p < 0.01) under OM treatment. The correlations between STN and its fractions were positively significant at 0–10 and 10–20 cm topsoil depths. Our results suggest that partial substitution of chemical fertilizer with organic manure could be a sustainable option for soil N management of intensive farming systems.

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